1. Field of the Invention
This invention relates generally to microarray technology for displaying and exploring gene expressions. More particularly, this invention is related a gene expression browser by presenting the gene expression profiles into two separate layers, the static and dynamic/responsive presentation layers in order to rapidly view the overall profiles on static data presentation layer, and search/highlight the detail data points in the dynamic responsive presentation layer.
2. Description of the Prior Art
The microarray gene expression data have accumulated in public repositories. The website of NCBI GEO (Gene Expression Omnibus at http://www.ncbi.nlm.nih.gov/geo had collected and annotated 279,089 samples from 10,964 series (experiments) by Jan. 25, 2009. Large amount of raw data and experimental annotations are classified and archived on GEO or EBI servers and are freely available to public. An effective and convenient tool to process and explain the microarray expression data in order to extract meaningful correlations and functional implications to fully utilize and maximize the values of the data becomes a critical issue facing the scientific, research, and medical communities.
Over the past few years, significant efforts have been devoted to develop the micoarray data mining and analysis tools, such as Spotfire, Rosetta Resolver, GeneSpring, TIGR TM4 (Saeed et. al, 2003), Genevestigator (Zimmermann et. al., 2004), Expression Profiler (Kapushesky et. al., 2004), NCBI GEO (Barrett et al., 2005). However, these tools are still difficult to operate due to the complexity in both statistic analysis methods and the large sale of the data. Furthermore, the analysis results are still displayed with heatmaps or x-y plot that is often shown only with limited scopes. Large amount of analysis results are usually shown without dynamically adjustable functional annotations. Therefore, the analytical and mining tools are not intuitive and difficult to comprehend and visualize the correlations between large amount of data even aided with these analysis and display tools. In order to overcome these difficulties, GeneChaser (Chen et. al., 2008) implements a software tool to search and display partial data in text table or bar graphics. The tables and bar graphics show provide simplified data analysis for direct and more intuitive visualization. However, the tool is still limited by the partial search scopes and cannot provide a general overall analysis and display capabilities to enable a dynamic, intuitive and comprehensive visualization of the data correlations among large amount of data now accumulated in the available databases.
As background of this invention, the references listed below provide further references that are relevant to the invention of this Patent Application.